5UTA

Sperm whale myoglobin H64Q with nitrite

5UTA の概要

• エントリーDOI: 10.2210/pdb5uta/pdb
• 関連するPDBエントリー: 5UT7 5UT8 5UT9 5UTB 5UTC 5UTD
• 分子名称: Myoglobin, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION, ... (6 entities in total)
• 機能のキーワード: heme, myoglobin, nitrite, nitrosyl, nitric oxide, oxygen transport
• 由来する生物種: Physeter catodon (Sperm whale)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 18808.00

構造登録者

Wang, B.,Thomas, L.M.,Richter-Addo, G.B. (登録日: 2017-02-14, 公開日: 2018-02-28, 最終更新日: 2024-03-06)

主引用文献

Wang, B.,Shi, Y.,Tejero, J.,Powell, S.M.,Thomas, L.M.,Gladwin, M.T.,Shiva, S.,Zhang, Y.,Richter-Addo, G.B.
Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets.
Biochemistry, 57:4788-4802, 2018

PubMed Abstract: The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) Mb and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) Mb and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The Mb-mediated reductions of nitrite to NO and structural data for the wt and mutant Mb-NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.

PubMed: 29999305
DOI: 10.1021/acs.biochem.8b00542

実験手法

X-RAY DIFFRACTION (1.81 Å)